Graduate Thesis Or Dissertation
 

Supplemental File. Next-generation sequencing.xlsx

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  • In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways.
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  • 2018-04-18 to 2019-09-21

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file details Supplemental_File._Next-generation_sequencing.xlsx 2018-04-18 Public Download